For Monkey Island 2 and all newer SCUMM games, iMUSE was used which makes the music change dynamically based on your actions in the game so the MIDI files can't be simply replaced with digital audio equivalents.

Loom on the other hand uses a regular, static MIDI soundtrack so replacing it using ScummVM would be possible if the developers of ScummVM added support for it. This isn't going to happen as my soundtracks aren't officially endorsed by LucasArts.